9D3B: Glutamate receptor ionotropic, NMDA 1

Gly-,Glu-,(S)-DQP-997-74 bound GluN1a-2B-2D NMDAR. Determined by electron microscopy at 3.71 Å resolution. Released 26 Feb 2025.

Method: Electron microscopy
Resolution: 3.71 Å
Organism: Homo sapiens
Chains: 4
Atoms: 23,783
Mol. weight: 380.23 kDa
Ligands: A1A15, GLU, NAG, GLY
Released: 26 Feb 2025

Explore 9D3B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D3B contains 136 α-helices and 140 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 35 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	26-33	8	1
α-helix	36-50	15
β-strand	59-66	8	1
α-helix	73-76	4
α-helix	83-85	3
β-strand	90-92	3	1
α-helix	105-113	9
β-strand	119-120	2	1
α-helix	127-129	3
β-strand	139	1	1
α-helix	144-151	8
α-helix	152-155	4
β-strand	165-168	4	2
α-helix	171-177	7
β-strand	194-197	4	2
α-helix	204-207	4
α-helix	209-213	5
β-strand	220	1	3
α-helix	225-232	8
β-strand	248	1	3
α-helix	262-263	2
β-strand	269-271	3	4
α-helix	277-295	19
α-helix	303-305	3
α-helix	319-325	7
β-strand	341	1	5
β-strand	345	1	5
β-strand	351-353	3	4
β-strand	356	1	6
β-strand	361	1	6
β-strand	365-367	3	7
β-strand	372-374	3	7
α-helix	378-379	2
α-helix	388-389	2
β-strand	397-402	6	8
β-strand	410-413	4	8
β-strand	424	1	9
β-strand	430	1	9
α-helix	431-432	2
β-strand	434-438	5	8
β-strand	451-456	6	8
α-helix	458-469	12
β-strand	473-478	6	8
β-strand	487-489	3	10
β-strand	496-498	3	10
α-helix	500-506	7
β-strand	512-513	2	8
β-strand	528	1	11
β-strand	538-542	5	12
α-helix	560-580	21
α-helix	603-606	4
α-helix	611-615	5
α-helix	627-656	30
α-helix	660-662	3
β-strand	682	1	12
β-strand	684	1	13
α-helix	689-695	7
α-helix	697-699	3
α-helix	700-706	7
β-strand	711	1	13
α-helix	716-721	6
β-strand	728-732	5	12
α-helix	733-742	10
β-strand	748-749	2	12
β-strand	761	1	8
β-strand	762	1	11
α-helix	769-779	11
α-helix	784-788	5
α-helix	789-794	6
α-helix	817-819	3
α-helix	820-836	17

Chain B: 36 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	35-41	7	14
α-helix	47-54	8
β-strand	66-72	7	14
α-helix	78-89	12
β-strand	97-100	4	14
α-helix	109-111	3
α-helix	113-118	6
β-strand	123-125	3	14
α-helix	128-130	3
β-strand	144-145	2	14
α-helix	151-154	4
α-helix	157-163	7
β-strand	168-172	5	15
α-helix	179-191	13
β-strand	198-203	6	15
α-helix	213-215	3
α-helix	217-221	5
β-strand	227-230	4	15
α-helix	234-247	14
β-strand	255-258	4	15
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	15
α-helix	289-310	22
α-helix	333-337	5
β-strand	343-344	2	16
β-strand	347-348	2	16
β-strand	362-367	6	15
β-strand	373-380	8	15
β-strand	383-385	3	15
β-strand	405	1	17
β-strand	409-410	2	18
β-strand	418-421	4	18
α-helix	422-423	2
β-strand	434-438	5	18
β-strand	453-458	6	18
α-helix	460-472	13
β-strand	475	1	17
β-strand	479-480	2	18
β-strand	490	1	19
β-strand	493	1	19
α-helix	498-501	4
β-strand	508-509	2	18
α-helix	517-520	4
β-strand	524-525	2	18
β-strand	534-536	3	20
β-strand	537-538	2	21
α-helix	558-560	3
α-helix	562-580	19
α-helix	605-611	7
α-helix	630-655	26
α-helix	669-672	4
α-helix	690-693	4
α-helix	695-697	3
α-helix	700-706	7
α-helix	707-709	3
α-helix	714-723	10
β-strand	730-732	3	20
α-helix	736-741	6
α-helix	744-746	3
β-strand	749-750	2	21
β-strand	765-766	2	18
α-helix	773-786	14
α-helix	789-796	8
α-helix	815-834	20
α-helix	835-839	5
α-helix	840-843	4

Chain C: 35 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	22
β-strand	31-32	2	23
α-helix	37-39	3
α-helix	42-50	9
β-strand	64-65	2	23
α-helix	71-77	7
α-helix	78-82	5
α-helix	83-85	3
β-strand	87	1	22
β-strand	91-92	2	24
α-helix	104-113	10
β-strand	119-120	2	24
β-strand	138-139	2	24
α-helix	142-143	2
α-helix	144-147	4
α-helix	148-158	11
β-strand	164	1	25
β-strand	165-166	2	26
β-strand	167-168	2	27
α-helix	171-181	11
β-strand	193	1	25
β-strand	196-197	2	27
α-helix	208-211	4
β-strand	220-221	2	26
α-helix	225-234	10
β-strand	247	1	28
β-strand	248-249	2	26
α-helix	252-254	3
α-helix	256-259	4
β-strand	266	1	28
α-helix	278-295	18
α-helix	302-305	4
α-helix	322-326	5
β-strand	356	1	29
β-strand	361	1	29
β-strand	366-367	2	30
β-strand	371-372	2	30
α-helix	378-380	3
α-helix	382-384	3
β-strand	398-402	5	31
β-strand	405	1	31
β-strand	409-412	4	31
β-strand	424	1	32
α-helix	429	1
β-strand	430	1	32
α-helix	431-432	2
β-strand	434-440	7	31
β-strand	449-457	9	31
α-helix	458-470	13
β-strand	474-478	5	31
β-strand	486	1	33
β-strand	499	1	33
α-helix	501-507	7
β-strand	512-513	2	31
α-helix	523-525	3
β-strand	527-528	2	31
β-strand	537	1	34
β-strand	538-543	6	35
α-helix	561-577	17
α-helix	607-615	9
α-helix	627-654	28
α-helix	670-673	4
β-strand	681-682	2	35
α-helix	688-695	8
α-helix	703-706	4
α-helix	714-722	9
β-strand	728-732	5	35
α-helix	733-742	10
β-strand	746-749	4	35
β-strand	755	1	34
β-strand	761-763	3	31
α-helix	769-781	13
α-helix	784-792	9
α-helix	812-838	27

Chain D: 30 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	54-56	3	36
α-helix	60-62	3
α-helix	63-74	12
β-strand	87-88	2	36
α-helix	102-105	4
α-helix	106-110	5
β-strand	115-117	3	36
α-helix	124-126	3
α-helix	127-137	11
β-strand	141-143	3	36
β-strand	161-163	3	36
α-helix	170-181	12
β-strand	186	1	37
β-strand	188-189	2	38
α-helix	197-208	12
β-strand	216	1	37
α-helix	229-235	7
β-strand	243-246	4	38
α-helix	253-262	10
β-strand	271-274	4	38
α-helix	300-301	2
β-strand	304-307	4	38
α-helix	317-335	19
α-helix	344-346	3
β-strand	368-369	2	39
β-strand	372-373	2	39
β-strand	376	1	40
β-strand	381	1	36
β-strand	382	1	40
β-strand	386-393	8	38
β-strand	397-405	9	38
β-strand	431-435	5	41
β-strand	439	1	41
β-strand	443-447	5	41
α-helix	448-449	2
α-helix	455-456	2
β-strand	460-463	4	41
β-strand	482-486	5	41
α-helix	488-498	11
β-strand	502-506	5	41
β-strand	516	1	42
β-strand	521	1	42
α-helix	523-529	7
β-strand	535-536	2	41
β-strand	541	1	43
α-helix	545-549	5
β-strand	562-566	5	44
α-helix	585-606	22
α-helix	629-639	11
α-helix	654-683	30
β-strand	711	1	44
α-helix	717-724	8
α-helix	727-733	7
α-helix	742-749	8
β-strand	756-758	3	44
α-helix	763-766	4
α-helix	771-773	3
β-strand	775-777	3	44
β-strand	789	1	43
β-strand	792	1	41
α-helix	800-810	11
α-helix	816-823	8
α-helix	849-852	4
α-helix	855-871	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 1	A, C	protein	825	Homo sapiens	Q05586 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2B	B	protein	884	Homo sapiens	Q13224 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2D	D	protein	861	Homo sapiens	O15399 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9D3B_1 Glutamate receptor ionotropic, NMDA 1 (chains A, C)
DPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLNATSVTHKPNAIQMALSVCEDL
ISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSFLRTVP
PYSHQSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRLETLLEERESKAEKVLQFDPGTK
NVTALLMEAKELEARVIILSASEDDAATVYRAAAMLNMTGSGYVWLVGEREISGNALRYA
PDGILGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFK
RVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRKLVQVGIYNGTHVIPNDRKIIWP
GGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDT
SPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMM
GELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTL
WLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSGIGEG
APRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYA
TVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQ
KCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDSRS
NAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRHKDANGAQ

Sequence of entity 2 (B), FASTA

>9D3B_2 Glutamate receptor ionotropic, NMDA 2B (chains B)
WSHPQFEKGGGSGGGSGGSAWSHPQFEKGALVPRGRSQKSPPSIGIAVILVGTSDEVAIK
DAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMSDRKIQGVVFADDTDQEAIAQI
LDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFSI
VTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLY
CTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPAEFPTGLISVSYDEWDYGLPA
RVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNMLNRYLINVTFEGRNLSF
SEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVWPRMCPETEEQEDDHLSIVTL
EEAPFVIVESVDPLSGTCMRNTVPCQKRIVTENKTDEEPGYIKKCCKGFCIDILKKISKS
VKFTYDLYLVTNGKHGKKINGTWNGMIGEVVMKRAYMAVGSLTINEERSEVVDFSVPFIE
TGISVMVSRSNGTVSPSAFLEPFSADVWVMMFVMLLIVSAVAVFVFEYFSPVGYNRSLAD
GREPGGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLA
AFMIQEEYVDQVSGLSDKKFQRPNDFSPPFRFGTVPNGSTERNIRNNYAEMHAYMGKFNQ
RGVDDALLSLKTGKLDAFIYDAAVLNYMAGRDEGCKLVTIGSGKVFASTGYGIAIQKDSG
WKRQVDLAILQLFGDGEMEELEALWLTGICHNEKNEVMSSQLDIDNMAGVFYMLGAAMAL
SLITFISEHLFYWQFRHSFMGGPGSGATNFSLLKQAGDVEENPG

Sequence of entity 3 (D), FASTA

>9D3B_3 Glutamate receptor ionotropic, NMDA 2D (chains D)
FPEEAPGPGGAGGPGGGLGGARPLNVALVFSGPAYAAEAARLGPAVAAAVRSPGLDVRPV
ALVLNGSDPRSLVLQLCDLLSGLRVHGVVFEDDSRAPAVAPILDFLSAQTSLPIVAVHGG
AALVLTPKEKGSTFLQLGSSTEQQLQVIFEVLEEYDWTSFVAVTTRAPGHRAFLSYIEVL
TDGSLVGWEHRGALTLDPGAGEAVLSAQLRSVSAQIRLLFCAREEAEPVFRAAEEAGLTG
SGYVWFMVGPQLAGGGGSGAPGEPPLLPGGAPLPAGLFAVRSAGWRDDLARRVAAGVAVV
ARGAQALLRDYGFLPELGHDCRAQNRTHRGESLHRYFMNITWDNRDYSFNEDGFLVNPSL
VVISLTRDRTWEVVGSWEQQTLRLKYPLWSRYGRFLQPVDDTQHLTVATLEERPFVIVEP
ADPISGTCIRDSVPCRSQLNRTHSPPPDAPRPEKRCCKGFCIDILKRLAHTIGFSYDLYL
VTNGKHGKKIDGVWNGMIGEVFYQRADMAIGSLTINEERSEIVDFSVPFVETGISVMVAR
SNGTVSPSAFLEPYSPAVWVMMFVMCLTVVAVTVFIFEYLSPVGYNRSLATGKRPGGSTF
TIGKSIWLLWALVFNNSVPVENPRGTTSKIMVLVWAFFAVIFLASYTANLAAFMIQEEYV
DTVSGLSDRKFQRPQEQYPPLKFGTVPNGSTEKNIRSNYPDMHSYMVRYNQPRVEEALTQ
LKAGKLDAFIYDAAVLNYMARKDEGCKLVTIGSGKVFATTGYGIALHKGSRWKRPIDLAL
LQFLGDDEIEMLERLWLSGICHNDKIEVMSSKLDIDNMAGVFYMLLVAMGLSLLVFAWEH
LVYWRLRHCLGPTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
A1A15	4-{(3R,5S)-5-(4-chlorophenyl)-3-[4-(4-chlorophenyl)-2-oxo-1,2-dihydroquinolin-3…	C28 H21 Cl2 F2 N3 O4	1
GLU	Glutamic acid	C5 H9 N O4	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
GLY	Glycine	C2 H5 N O2	2

Primary citation

Structural basis for channel gating and blockade in tri-heteromeric GluN1-2B-2D NMDA receptor. Kang, H., Epstein, M., Banke, T.G. et al. Neuron (2025) 113:991. DOI 10.1016/j.neuron.2025.01.013 · PubMed

Other PDB entries of the same protein (UniProt Q05586 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GJ1 1.62 Å, NMDA bound to compound 339
5H8F 1.81 Å, Structure of the apo human GluN1/GluN2A LBD
9GIC 1.82 Å, NMDA bound to compound 345
3BYA 1.85 Å, Structure of a Calmodulin Complex
5H8Q 1.9 Å, Structure of the human GluN1/GluN2A LBD in complex with GNE8324
9GIF 1.9 Å, NMDA bound to compound 288
9GIB 1.95 Å, NMDA bound to compound 380
9MUM 1.97 Å, Crystal structure of GluN1/GluN2A ligand-binding domain in complex with Compound 11,…
9GID 2.0 Å, NMDA bound to compound 338
5KCJ 2.09 Å, Structure of the human GluN1/GluN2A LBD in complex with GNE6901
9GIG 2.09 Å, NMDA bound to compound 387
5I2N 2.12 Å, Structure of the human GluN1/GluN2A LBD in complex with…

Browse structure collections

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